The invention relates to fusion proteins, DNA molecules encoding the fusion proteins, vectors comprising the DNA molecules, host cells transformed with the vectors, and methods and kits for using them to determine the activity of a protease. Specifically, the invention relates to a fusion protein having a protease cleavage site, a ligand-binding domain, and a DNA-binding domain, wherein (1) the association of a ligand with the ligand-binding domain of said fusion protein mediates the binding of the DNA-binding domain of said fusion protein to a ligand-response element (xe2x80x9cLRExe2x80x9d) that is operatively linked to a reporter gene; and wherein (2) the fusion protein comprises an expression modulator domain or associates with a second protein having an expression modulator domain, wherein said expression modulator domain regulates transcription of the reporter gene. The invention also relates to kits for assaying protease activity comprising DNA molecules encoding the fusion proteins, an appropriate ligand, and DNA molecules comprising a promoter-reporter gene construct and at least one LRE recognized by the DNA binding domain of the fusion protein. The DNA molecules in these kits may be isolated or present in host cells.
Proteases play an important role in the regulation of biological processes in almost every life form from bacteria to virus to mammals. They perform critical functions in, for example, digestion, blood clotting, apoptosis, activation of immune responses, zymogen activation, viral maturation, protein secretion and protein trafficking.
Proteases have been implicated as the cause of or as contributors to several diseases such as Alzheimer""s disease, cystic fibrosis, emphysema, hypertension, tumor invasion and metastasis and viral-associated diseases [e.g., Kim, T. W., et al., (1997) xe2x80x9cAlternative Cleavage of Alzheimer-associated Presinilins During Apoptosis by a Caspase-3 Family Protease,xe2x80x9d Science 277:373-6; Lacana, E. et al., (1997) xe2x80x9cDisassociation of Apoptosis and Activation of IL-1 beta-converting Enzyme/Ced-3 Proteases by ALG-2 and the Truncated Alzheimer""s gene ALG-3,xe2x80x9d J. Immunol. 158:5129-35; Birrer, P., (1995) xe2x80x9cProteases and Antiproteases in Cystic Fibrosis: Pathogenic Considerations and Therapeutic Strategies,xe2x80x9d Respiration 62:25-8; Patel, T., et al., (1996) xe2x80x9cThe Role of Proteases During Apoptosis,xe2x80x9d FASEB J. 10:587-97].
Several viral genomes also encode proteases that are important in the viral maturation process. For example, the viral aspartyl protease of the Human Immunodeficiency Virus (HIV) cleaves a HIV polypeptide containing the Gag and Pol polyproteins.
In another example, the hepatitis C virus (HCV) produces a long polypeptide translation product, NH2-C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B-COOH, which is cleaved to produce at least 10 proteins. C, E1 and E2 are putative structural proteins, and the remainder are known as the nonstructural (NS) proteins. One of those proteins is NS3, a 70 kilodalton protein having serine protease activity. It is been shown that the protease activity of NS3 resides exclusively in the N-terminal 180 amino acids of the enzyme. The NS3 protease cleavages at four sites in the nonstructural region of the HCV polypeptide (3/4A, 4A/4B, 4B/5A, and 5A/5B). Another protein, NS4A, has 54 amino acids and has been characterized as a cofactor for the NS3 protease [C. Failla, et al., (1994) J. Virology 68:3753-3760]. The C-terminal 33 amino acids of NS4A are required for cleavage at the 3/4A site and 4B/5A sites and accelerate the rate of cleavage at the 5A/5B site. Several other NS3 serine protease-dependent cleavage site sequences have been identified in various strains of HCV [A. Grakoui, et al., (1993) J. Virology 67:2832-2843 incorporated by reference herein].
The ability to detect viral, cellular, or microorganism protease activity in a quick and simple assay is important in the biochemical characterization of these proteases, in detecting viral infection, and in the screening and identification of potential inhibitors.
Several protease assays are known in the art. T. A. Smith et al., Proc. Natl. Acad. Sci. USA, 88, pp. 5159-62 (1991); B. Dasmahapatra et al., Proc. Natl. Acad. Sci. USA, 89, pp. 4159-62 (1992); and M. G. Murray et al., Gene, 134, pp. 123-128 (1993) each describe protease assay systems utilizing the yeast GAL4 protein. Each of these documents describe inserting a protease cleavage site in between the DNA binding domain and the transcriptional activating domain of GAL4. Cleavage of that site by a coexpressed protease renders GAL4 transcriptionally inactive leading to the inablility of the transformed yeast to metabolize galactose.
Y. Hirowatari et al., Anal. Biochem., 225, pp. 113-120 (1995) describes an assay to detect HCV protease activity. In this assay, the substrate, HCV protease and a reporter gene are cotransfected into COS cells. The substrate is a fusion protein consisting of (HCV NS2)(DHFR)-(HCV NS3 cleavage site)-Tax1. The reporter gene is chloramphenicol transferase (CAT) under control of the HTLV-1 long terminal repeat (LTR) and resides in the cell nucleus following expression. The uncleaved substrate is expressed as a membrane-bound protein on the surface of the endoplasmic reticulum due to the HCV NS2 portion. Upon cleavage, the released Tax1 protein translocates to the nucleus and activates CAT expression by binding to the HTLV-1 LTR. Protease activity is determined by measuring CAT activity in a cell lysate.
Each of the assays described above requires simultaneous (1) expression of an active protease and a substrate and (2) transcription of a reporter gene construct. The constitutive nature of these assays can often produce uncontrollable and undesirable effects. These effects may give rise to misleading or inaccurate conclusions regarding the activity of the protease. Thus, there is a need for a sensitive and quantitative protease assay that is inducible or can be readily controlled by the user.
The present invention fulfills this need by providing novel fusion proteins, DNA molecules encoding them, vectors comprising the DNA molecules, and host cells containing the vectors useful in a fusion protein ligand-dependent transcriptional assay to determine the activity of a protease.
The novel fusion protein comprises a protease cleavage site, a ligand-binding domain, and a DNA-binding domain, wherein (1) the association of a ligand with the ligand-binding domain of said fusion protein mediates the binding of the DNA-binding domain of said fusion protein to a LRE that is operatively linked to a reporter gene; and wherein (2) the fusion protein comprises an expression modulator domain or associates with a second protein having an expression modulator domain, wherein said expression modulator domain regulates the transcription of the reporter gene.
According to the methods of this invention, the binding of a ligand to the ligand binding domain of the uncleaved fusion protein initiates the activation or repression of transcription of the reporter gene at a discrete point in time. This inducibility allows the assay to be better controlled and therefore, produces more accurate results.
Cleavage of the fusion protein at the protease cleavage site deregulates transcription of the reporter gene by preventing the expression modulator domain from modulating transcription positively or negatively. The amount of cleaved fusion protein is quantitated by assaying an increase or decrease in transactivation of a reporter gene, whose expression is driven by a promoter which is modulated by the expression modulating domain of the fusion protein.
This invention also relates to a method for measuring the inhibitory activity of a compound against a protease comprising the steps of incubating the fusion protein with a protease in the presence or absence of a compound whose activity is being tested, adding a ligand to the incubation and quantifying the gene product produced from a reporter gene.
Yet another embodiment of this invention relates to a method for comparing the activity of two proteases or mutants of a protease which recognize the same cleavage site.
The Invention also relates to kits for assaying protease activity comprising DNA molecules encoding the fusion protein, the fusion protein or host cells containing the DNA molecules, wherein the kit optionally includes DNA molecules encoding a protease, DNA molecules comprising a reporter gene whose expression is regulated by said fusion protein, a ligand which associates and regulates the activity of said fusion protein, and instructions for using said kit. Preferably, the DNA molecules in the kit have been engineered into a vector that allows their expression. A kit according to this invention, may comprise any one or all of the following DNA molecules transformed into a single host cell selected from the group consisting of: a DNA molecule encoding a fusion protein of this invention, a DNA molecule encoding a protease, a DNA molecule encoding a protein binding partner for the fusion protein and a DNA molecule comprising a promoter-reporter gene construct.